Advancements in automated photovoltaic solar cell manufacturing are enabling higher throughput, yield, and cell conversion efficiencies. For example, commercially available automated equipment for applying conductive layers to crystalline silicon solar cells routinely screen print the metallization at a rate of one cell per second. Newer technologies for improving cell conversion efficiencies such as the selective emitter process, metal-wrap-through, and print-on-print are being adopted that require precise registration of the metallization layers. Cell efficiencies are also affected by the height to width ratio of the metalized collector fingers, which collect the electric current generated by the solar cell. These fingers must be printed narrowly in width to avoid unnecessary shading of the cell active area, but must also be printed tall in height to improve electrical conductivity. Also, the fragility of the thin silicon solar cells and their tendency to bow during manufacturing, presents challenges to the automated handling equipment to avoid chips and cracks. Bowed wafers may crack, for example, when they are vacuum secured during one of the many manufacturing process steps or when pressure is applied to the wafer during the screen printing process. In view of these industry demands, a need has arisen for automated optical inspection systems that are distributed throughout the solar cell manufacturing process to ensure high process yield. Given the increased needs for precision registration, narrower and taller features, and detection of wafer bowing, it would be beneficial to provide an automated optical inspection system that was not only faster than the prior art, but also better able to provide higher resolution two and three dimensional inspection of the solar cells.